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[…] entrifugation of whole blood, plasma was obtained and frozen at −80°C., Fifteen HLA-A*02-restricted HCV epitopes (supplementary table 2 online) were chosen using the predominant amino acid sequences which were either present in the donor (GenBank: AF313916) or circulating in the recipients. Control epitopes from influenza, cytomegalovirus (CMV) and Epstein–Barr virus (EBV) were also chosen (Supplementary table 2). A set of 300 20mer overlapping peptides (average purity 86%) were used (Pro-immune, Oxford, UK) and were based on the genotype 1b donor sequence (GenBank: AF313916)., Predicted epitopes were identified using a combination of different prediction programs (Bimas, SYFPEITHI, Jenner, ProPred 1, Rankpep, MAPPP and Net MHC). Epitopes with the highest ranking were chosen (supplementary table 1 online). In order to generate CD8 T cell lines, we stimulated PBMCs with three of the predicted HLA-A*03-restricted HCV epitopes and two EBV-derived epitopes. These were the two ‘footprint’ epitopes NS3 1080–1088 TVYHGAGTK and NS5B 2510–2518 KLTPPHSAK and also a third non-‘footprint’ epitope NS5B 2562–2570 EVFCVQPEK. The control peptides were RLRAEAQVK and RVRAYTYSK (see supplementary table 1 for more details)., Sera samples from cohort subjects were collected between 1996 and 2002 and stored at −80°C (St James' Hospital, Dublin, Ireland). Stored patient sera were available on 15 previously identified HL […]

Pipeline specifications

Software tools ProPred, RANKPEP, MAPPP
Databases SYFPEITHI